Provided by: rambo-k_1.21+dfsg-2_all
rambo-k - Read Assignment Method Based On K-mers
rambo-k [-h] -r REFFILE1 -R REFFILE2 [-n NAME1] [-N NAME2] -1 UNASSIGNED1 [-2 UNASSIGNED2] [-k KMERSIZES] [-o OUTPATH] [-a AMOUNT] [-t THREADS] [-x CHUNKSIZE] [-g GAPSIZE] [-c CUTOFF_LOWER] [-C CUTOFF_HIGHER] [-d] [-f FILETYPE]
RAMBO-K is a reference-based tool for rapid and sensitive extraction of one organisms reads from a mixed dataset. It is based on a Markov chain implementation, which uses genomic characteristics of each reference to assign reads to the associated set.
-h, --help show this help message and exit -r REFFILE1, --reffile1 REFFILE1 Reference file of species 1 in fasta-format. Should pair with name1 -R REFFILE2, --reffile2 REFFILE2 Reference file of species 2 in fasta-format. Should pair with name2 -n NAME1, --name1 NAME1 Name of species 1 -N NAME2, --name2 NAME2 Name of species 2 -1 UNASSIGNED1, --unassigned1 UNASSIGNED1 Fasta- or fastq-file containing mixed reads. -2 UNASSIGNED2, --unassigned2 UNASSIGNED2 Fasta- or fastq-file containing mixed reads, only required in paired end mode. -k KMERSIZES, --kmersizes KMERSIZES Order of Markov-Chain/kmer length. Enter as range (e.g. 4:8) or list (e.g. 4,6,8) or integer (e.g. 8). Default = 8 -o OUTPATH, --outpath OUTPATH Folder to write results to. Default = $name1_$name2/ in your working directory -a AMOUNT, --amount AMOUNT Number of reads to be simulated, default = 50000 -t THREADS, --threads THREADS Number of Threads to use -x CHUNKSIZE, --chunksize CHUNKSIZE Size of chunks created at a time for simulation, default = 100000. Only change if you know what you are doing! -g GAPSIZE, --gapsize GAPSIZE Estimated size of gapsize in case of paired end reads, default = 1 -c CUTOFF_LOWER, --cutoff_lower CUTOFF_LOWER Lower cutoff: Output only reads with a score lower than or equal to this value, use m1 for -1 -C CUTOFF_HIGHER, --cutoff_higher CUTOFF_HIGHER Higher cutoff: Output only reads with a score higher than or equal to this value, use m1 for -1 -d, --delete_temp \Delete temporary files. Calculations will start from beginning next time. -f FILETYPE, --filetype FILETYPE Type of your input reads. fasta or fastq, default = fastq
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.